The rest of the files: I have also check the exclusions with the csg_dump, again with the different versions. Using
csg_dumpp --top mma_trimer_sd_noexclusions.tpr --excl I got the same output for the three cases. Not sure what is happening. Cheers Nancy On Sunday, 27 December 2020 at 12:56:05 UTC+1 nancyfor wrote: > Hi Christoph, > > I have corrected the mapping file. However, when creating the > exclusion.txt I noticed this file was not correct. For this I generated a > .tpr file without exclusions > and use: > > csg_boltzmann --top mma_trimer_sd_noexclusions.tpr --cg > mma_trimer_mapping.xml --excl exclusions.txt > > I used votca 1.6.2. I tried two other versions of votca, sourcing someone > else installation, votca 1.6-dev and a local machine version. > > I supposed this is a problem with my installation. Is there a way to check > that votca was installed correctly? I did not get any error while > installing it. And I have not seen anyone with this problem browsing the > messages. > > I have attached the mapping file and the exclusion files for the different > votca versions. > > details of the versions below > > csg_boltzmann, version 1.6.2 gitid: 9b6bbd0 (compiled Dec 19 2020, > 15:56:40) > votca_tools, version 1.6.2 gitid: 9b6bbd0 (compiled Dec 19 2020, 15:55:42) > gromacs, 2019.4 (single precision) > > > csg_boltzmann, version 1.6-dev gitid: e42c3e100 (compiled Jun 30 2020, > 17:41:20) > votca_tools, version 1.6-dev gitid: e42c3e100 (compiled Jun 30 2020, > 17:40:52) > gromacs, 2019.4 (single precision) > > > csg_boltzmann, version 1.5 (compiled Feb 8 2019, 02:59:36) > votca_tools, version 1.5 (compiled Feb 8 2019, 02:57:53) > gromacs, 2019.1 (double precision) > > On Sunday, 27 December 2020 at 10:18:45 UTC+1 nancyfor wrote: > >> Thanks Christoph, I completely overlooked this. >> Cheers, >> Nancy >> >> On Sunday, 27 December 2020 at 01:23:11 UTC+1 Christoph Junghans wrote: >> >>> On Sat, Dec 26, 2020 at 4:29 PM nancyfor <[email protected]> wrote: >>> > >>> > Hello everybody, >>> > >>> > I am trying to get the probability distribution functions and the >>> tabulated potentials for a system with 11 coarse grained beads. However >>> when listing all available bonded interaction only list 3. Coincidentally, >>> they are the last bonded interactions for angle, bond and dihedral sections >>> respectively. I am using votca 1.6.2 and gromacs 2019.4 >>> > >>> > This is the output for >>> > >>> > csg_boltzmann --top topol.tpr --trj traj.xtc --cg mapping.xml >>> > list >>> > >>> > Available bonded interactions: >>> > molecule 0:EMBT:index 0 >>> > molecule 0:MBT:index 0 >>> > molecule 0:SMEMBT:index 0 >>> > >>> > I have checked if the mapping was correct using csg_dump, and it seems >>> is fine. >>> > >>> > I have attached the mapping file in case you spot any mistake. >>> Yeah, you need to put each bond, angle, dihedral in its own <bond>, >>> <angle>, <dihedral> block, otherwise all properties (name, beads etc) >>> will be overwritten by the latest entry and hence you end up with one >>> of each. >>> >>> If the documentation is unclear on that, please modify the >>> input_files.rst file in the share/doc folder of the csg module and >>> send up as a patch or submit a pull request on GitHub. >>> >>> Christoph >>> >>> > Best regards, >>> > Nancy >>> > >>> > -- >>> > Join us on Slack: https://join.slack.com/t/votca/signup >>> > --- >>> > You received this message because you are subscribed to the Google >>> Groups "votca" group. >>> > To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> > To view this discussion on the web visit >>> https://groups.google.com/d/msgid/votca/561b4631-045c-45d6-b3b7-b9ee61646d4fn%40googlegroups.com. >>> >>> >>> >>> >>> >>> -- >>> Christoph Junghans >>> Web: http://www.compphys.de >>> >> -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/58e38a35-6a98-422f-8282-c02f2c7f95c8n%40googlegroups.com.
# atomistic: 3-MMA cg: 3-MMA cgmap: mma_trimer_mapping.xml 1 42 43 44 45 2 42 43 44 45 3 42 43 44 45 4 42 43 44 45 5 42 43 44 45 6 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51 7 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51 8 25 26 27 28 29 30 31 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 9 25 26 27 28 29 30 31 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 10 25 26 27 28 29 30 31 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 11 25 26 27 28 29 30 31 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 12 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51 13 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51 14 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51 15 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51 16 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51 17 42 43 44 45 18 42 43 44 45 19 42 43 44 45 25 42 43 44 45 26 42 43 44 45 27 40 41 42 43 44 45 46 48 49 50 51 28 40 41 42 43 44 45 46 48 49 50 51 29 40 41 42 43 44 45 46 48 49 50 51 30 40 41 42 43 44 45 46 48 49 50 51 31 42 43 44 45
# atomistic: 3-MMA cg: 3-MMA cgmap: mma_trimer_mapping.xml 1 42 43 44 45 2 42 43 44 45 3 42 43 44 45 4 42 43 44 45 5 42 43 44 45 6 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51 7 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51 8 25 26 27 28 29 30 31 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 9 25 26 27 28 29 30 31 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 10 25 26 27 28 29 30 31 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 11 25 26 27 28 29 30 31 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 12 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51 13 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51 14 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51 15 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51 16 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51 17 42 43 44 45 18 42 43 44 45 19 42 43 44 45 25 42 43 44 45 26 42 43 44 45 27 40 41 42 43 44 45 46 48 49 50 51 28 40 41 42 43 44 45 46 48 49 50 51 29 40 41 42 43 44 45 46 48 49 50 51 30 40 41 42 43 44 45 46 48 49 50 51 31 42 43 44 45
I have 53 beads in 1 molecules List of exclusions: 1 2 3 4 5 6 7 8 12 13 14 15 16 17 18 19 20 21 25 32 2 3 4 5 6 7 12 13 14 15 16 17 18 19 20 3 4 5 6 13 17 4 5 6 13 17 5 6 13 17 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 7 8 9 10 11 12 13 17 8 9 10 11 12 9 10 11 10 11 12 13 17 13 14 15 16 17 18 19 20 14 15 16 17 15 16 17 16 17 17 18 19 20 21 22 23 24 25 26 31 32 33 34 35 18 19 20 21 25 32 19 20 21 25 32 20 21 22 23 24 25 26 27 31 32 33 34 35 36 40 47 21 22 23 24 25 26 31 32 33 34 35 22 23 24 25 32 23 24 25 32 24 25 32 25 26 27 28 29 30 31 32 33 34 35 26 27 28 29 30 31 32 27 28 29 30 31 28 29 30 29 30 31 32 32 33 34 35 36 37 38 39 40 41 46 47 48 52 53 33 34 35 36 40 47 34 35 36 40 47 35 36 37 38 39 40 41 42 46 47 48 49 50 51 52 53 36 37 38 39 40 41 46 47 48 52 53 37 38 39 40 47 38 39 40 47 39 40 47 40 41 42 43 44 45 46 47 48 52 53 41 42 43 44 45 46 47 42 43 44 45 46 43 44 45 44 45 46 47 47 48 49 50 51 52 53 48 49 50 51 52 53 49 50 51 52 53 50 51 52 53 51 52 53 52 53
